rs1368402

Variant names:

• chr5-146337722-A-C
• rs1368402
• ENST00000506502.2:c.2947-1381A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001414499.1(RBM27-POU4F3):​c.2824-1381A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,020 control chromosomes in the GnomAD database, including 8,370 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.30 (8370 hom., cov: 32)
• Consequence: RBM27-POU4F3 NM_001414499.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 11 publications found

Genes affected

ENSG00000275740 (HGNC:58349):

ENSG00000250025 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001414499.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBM27-POU4F3	NM_001414499.1		c.2824-1381A>C		intron	N/A	NP_001401428.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000275740	ENST00000506502.2	TSL:5	c.2947-1381A>C		intron	N/A	ENSP00000475384.1	U3KPZ7
	ENSG00000250025	ENST00000515598.1	TSL:3	n.404-30446T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45612 AN: 151902 Hom.: 8341 Cov.: 32

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.274

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.301 AC: 45686 AN: 152020 Hom.: 8370 Cov.: 32 AF XY: 0.296 AC XY: 21969 AN XY: 74288

African (AFR) AF: 0.524 AC: 21730 AN: 41442

American (AMR) AF: 0.204 AC: 3125 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 855 AN: 3472

East Asian (EAS) AF: 0.218 AC: 1123 AN: 5152

South Asian (SAS) AF: 0.128 AC: 619 AN: 4820

European-Finnish (FIN) AF: 0.224 AC: 2367 AN: 10556

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14867 AN: 67974

Other (OTH) AF: 0.271 AC: 573 AN: 2112

Alfa AF: 0.237 Hom.: 7281

Bravo AF: 0.314

Asia WGS AF: 0.197 AC: 684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.5
DANN	Benign	0.65
PhyloP100		0.011
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1368402; hg19: chr5-145717285;